Could there be a problem because I installed .NET 3.0 Framework? But in the MRefBuilder.config the 2.0 Version is listed correctly: <platform version="2.0" path="%SystemRoot%\Microsoft.NET\Framework\v2.0.50727\" />

The .NET 2.0 framework is also used for documenting .NET 3.0 projects. It's the same but with a few extra assemblies. Your problem is most likely caused by the VB.NET compiler. If you check the XML comments file for the failing <see> tags, you will
probably find that it isn't fully qualifying the member name (i.e. it's missing a prefix and/or namespace). For example instead of <see cref="P:MyNamespace.MyClass.MyProperty"/> it will be listed as <see cref="MyProperty"/> or <see cref="MyNamespace.MyClass.MyProperty"/>.
To "fix" it, you have to specify the fully qualified name including the prefix and the namespace. Use "T:" for types, "M:" for methods, "P:" for properties, and "E:" for events.